Dear FreeSurfur Gurus, It appears that the using -use-mritotal worked to get past the talairach error.
Thank you for all your help. We really appreciate it. Joshua On Wed, Nov 2, 2011 at 7:01 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Michael > > we found that the conversion to unsigned character sometimes compressed > the brain into only a couple of bits of the dynamic range. We know use the > talairach xform to locate the center of the brain and make sure that a ball > centered at the tal origin occupies a lot of the histogram. This helped in > a number of cases, but maybe the makes the tal xform more sensitive to bias > fields and strange intensity scalings. > > Bruce > > On Wed, 2 Nov 2011, Michael Waskom wrote: > > Hi, >> What was the reason for this switch? Intuitively it seems that a >> bias-corrected image is likely to get a better registration (since I >> assume the target has essentially uniform intensities). >> >> Michael >> >> On Wed, Nov 2, 2011 at 1:15 PM, Nick Schmansky <ni...@nmr.mgh.harvard.edu> >> wrote: >> no, v5.0 uses nu.mgz as input to the talairach_avi routine, whereas >> v5.1 >> uses orig.mgz. >> >> its hard to say why it would fail for some subjects but not others, >> other than head positioning and to some degree ventricle size makes a >> difference. >> >> n. >> >> On Wed, 2011-11-02 at 16:10 -0400, Joshua Lee wrote: >> > Thanks Nick, >> > >> > Is use-mritotal equivalent to what version 5.0 does by default? >> > >> > Also, any suggestions on why this talairach error would occur only on >> > a portion of my data, despite all being collected with the same >> > imaging protocol, same conversions from dicom, etc? >> > - >> > >> > Joshua Lee >> > >> > Graduate Student >> > Center for Mind and Brain & >> > >> > Department of Psychology >> > >> > University of California, Davis >> > 530.747.3805 >> > >> > >> > On Wed, Nov 2, 2011 at 4:02 PM, Nick Schmansky >> > <ni...@nmr.mgh.harvard.edu> wrote: >> > joshua, >> > >> > try adding -use-mritotal to the end of your recon-all >> > command. it will >> > use an alternate way to compute the talairach.xfm which works >> > better on >> > some data. >> > >> > the change from v5.0 to v5.1 in the talairach stage was that >> > in v5.1, >> > the talairach.xfm is needed to compute nu.mgz, so the >> > talairach stage >> > needs to precede the nu_correct stage. this means the >> > talairach stage >> > can no longer use nu.mgz as input, which seems to work better >> > than >> > orig.mgz for some data (and is the case for your data). >> > >> > in the next release of freesurfer, recon-all will >> > automatically try the >> > alternate method (mritotal) if the default talairach_avi >> > method fails >> > the tal-check. >> > >> > n. >> > >> > >> > >> > On Wed, 2011-11-02 at 08:45 -0400, Bruce Fischl wrote: >> > > can you send us an example that works in 5.0 and fails in >> > 5.1? >> > > >> > > thanks >> > > Bruce >> > > On Wed, 2 Nov >> > > 2011, Joshua Lee wrote: >> > > >> > > > Small Update: Error Disappears if Using Freesurfer version >> > 5.0 instead of >> > > > 5.1. However, since I am keenly interested in the >> > hippocampal-subfield >> > > > segmentation capabilities of the most recent version, I am >> > loathe to regress >> > > > to an earlier version of FreeSurfer >> > > > - >> > > > Joshua Lee >> > > > Graduate Student >> > > > Center for Mind and Brain & >> > > > Department of Psychology >> > > > University of California, Davis >> > > > 530.747.3805 >> > > > >> > > > >> > > > On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee >> > <jki...@ucdavis.edu> wrote: >> > > > #@# Talairach Failure Detection Wed Nov 2 02:03:32 >> > EDT 2011 >> > > > /home/virtualuser/freesurfer/**subjects/test005/mri >> > > > >> > > > talairach_afd -T 0.005 -xfm >> > transforms/talairach.xfm >> > > > >> > > > I am receiving the error (pasted below) on about >> > half of my >> > > > scans, despite all cans using same protocol. I >> > detect no obvious >> > > > issue with the quality of the images. I have >> > original dicoms, >> > > > and am using mri_convert to save into a single .mgz >> > (or .nii, >> > > > doesn't neem to make a difference), and the >> > unpredictability of >> > > > the error makes diagnosis problematic. TKMedit2 >> > reveals >> > > > absolutely wacky registrations. I am processing on >> > Freesurfer >> > > > 5.1, and have replicated issue on two different >> > installations. I >> > > > am designing a new longitudinal study inheriting the >> > same >> > > > imaging protocol and I do not want to get in a >> > situation >> > > > demanding manual editing of the talairach. Can >> > anyone help me >> > > > out? Thanks, Joshua >> > > > >> > > > ERROR: talairach_afd: Talairach Transform: >> > > > transforms/talairach.xfm ***FAILED*** (p=0.0030, >> > pval=0.0000 < >> > > > threshold=0.0050) >> > > > Manual Talairach alignment may be necessary, or >> > > > include the -notal-check flag to skip this test, >> > > > making sure the -notal-check flag follows -all >> > > > or -autorecon1 in the command string. >> > > > See >> > > > >> > http://surfer.nmr.mgh.harvard.**edu/fswiki/FsTutorial/** >> Talairach <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach> >> > > > Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP >> > Fri Apr 17 >> > > > 01:57:59 UTC 2009 i686 GNU/Linux >> > > > >> > > > recon-all -s test005 exited with ERRORS at Wed Nov >> > 2 02:03:32 >> > > > EDT 2011 >> > > > >> > > > For more details, see the log file >> > > > >> > /home/virtualuser/freesurfer/**subjects/test005/scripts/** >> recon-all.log >> > > > To report a problem, see >> > > > >> > >> > http://surfer.nmr.mgh.harvard.**edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > > > >> > > > - >> > > > Joshua Lee >> > > > Graduate Student >> > > > Center for Mind and Brain & >> > > > Department of Psychology >> > > > University of California, Davis >> > > > 530.747.3805 >> > > > >> > > > >> > > > >> > > > >> > >> > > ______________________________**_________________ Freesurfer >> > mailing list Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > >> > >> > >> > >> > The information in this e-mail is intended only for the person >> > to whom it is >> > addressed. If you believe this e-mail was sent to you in error >> > and the e-mail >> > contains patient information, please contact the Partners >> > Compliance HelpLine at >> > >> > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> > If the e-mail was >> > sent to you in error >> > but does not contain patient information, please contact the >> > sender and properly >> > dispose of the e-mail. >> > >> > >> > >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >>
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